createCNSummary {beadarraySNP} | R Documentation

## Summarization of Copy number states

### Description

Create a summary object of the genomic copy number states in a sample of segmented data

### Usage

    createCNSummary(object, sample, dnaIndex=1, subsample = "OPA")

### Arguments

`object` | SNPSetIllumina object after segmentation `segmentate`
`sample` | SampleName or index of the sample for which to create the summary
`dnaIndex` | Measured DNA index of the sample
`subsample` | factor or column name in `featureData` slot

### Details

The segments within a sample are assigned a copy number value. When the `inferred` slot in `assayData` is empty, all segments will be set to 2. Otherwise the values are recovered from the `inferred` slot. Gender is taken into account for the sex chromosomes.

### Value

list with the following elements

`dnaIndex` | same as parameter dnaIndex
`CN.total.nrm` | Total expected copynumber for a 'normal' specimen ~ 2*featurecount
`states` | data.frame with columns `opa, count ,intensity, copynumber`

This list can be used as the `cn.sum` argument for `plotGoldenGate4OPA, alterCN, getDNAindex` and `setRealCN`

### Author(s)

Jan Oosting

### See Also

`segmentate, alterCN, plotGoldenGate4OPA`

[Package beadarraySNP version 1.60.0 Index]